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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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1 <tool id="phytab_mafft" name="phytab MAFFT" force_history_refresh='True'>
2 <description> Multiple Sequence Alignment </description>
3 <requirements>
4 <requirement type="binary">mafft</requirement>
5 </requirements>
6 <command interpreter="python">
7 phytab_mafft.py -s $Strategy -i $input > $mafft_stdout 2>&amp;1
8 </command>
9 <inputs>
10 <param format="fasta,tabular" name="input" type="data" label="Sequence data" help="Format: Fasta or Phytab"/>
11 <param name="Strategy" type="select" label="Alignment Strategy">
12 <option value="Auto">Auto</option>
13 <option value="FFT-NS-1">FFT-NS-1</option>
14 <option value="FFT-NS-2">FFT-NS-2</option>
15 <option value="FFT-NS-i">FFT-NS-i</option>
16 <option value="E-INS-i">E-INS-i</option>
17 <option value="L-INS-i">L-INS-i</option>
18 <option value="G-INS-i">G-INS-i</option>
19 <option value="Q-INS-i">Q-INS-i</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data format="txt" name="mafft_stdout" label="${tool.name} on ${on_string}: stdout" />
24 <data from_work_dir="data/results.data" format="input" name="seqs_aligned" label="${tool.name} on ${on_string}: Screen Output" />
25 </outputs>
26 <tests>
27 </tests>
28 <help>
29 **What it does**
30 This tool runs MAFFT alignment algorithm on when given a single-gene (fasta or phytab) or a multi-gene (phytab) dataset.
31 Output for single genes is fasta; output for multi-genes is phytab.
32
33 ------
34
35 **Inputs**
36
37 FASTA (single-gene) or phytab (single- or multi-gene).
38
39 *Algorithm strategies:*
40
41 Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size; may vary between gene partitions in cases of multi-gene input datasets).
42
43 FFT-NS-1 (Very fast; recommended for more than 2,000 sequences; progressive method).
44
45 FFT-NS-2 (Fast; progressive method).
46
47 FFT-NS-i (Slow; iterative refinement method).
48
49 E-INS-i (Very slow; recommended for less than 200 sequences with multiple conserved domains and long gaps).
50
51 L-INS-i (Very slow; recommended for less than 200 sequences with one conserved domain and long gaps).
52
53 G-INS-i (Very slow; recommended for less than 200 sequences with global homology).
54
55 Q-INS-i (Extremely slow; secondary structure of RNA is considered; recommended for a global alignment of highly diverged ncRNAs with less than 200 sequences × less than 1,000 nucleotides).
56
57 ------
58
59 **Outputs**
60
61 phytab
62
63 ------
64
65 **Additional Information**
66
67 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org
68
69 -------
70
71 **Citations**
72
73 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.
74
75 Current Osiris Citation is here
76
77 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
78
79 Additional Citations for this tool
80
81 MAFFT: MAFFT: Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
82 Recent developments in the MAFFT multiple sequence alignment program.
83
84 MAFFT website: http://mafft.cbrc.jp/alignment/server/index.html
85 </help>
86 </tool>